Mercurial > repos > rdvelazquez > hyphy_fade

annotate test-data/meme-out1.json @ 7:a7305e34418f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:12:14 -0500
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7
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1 {
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2 "analysis":{
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3 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
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4 "version":"2.0.1",
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5 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
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6 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
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7 "contact":"spond@temple.edu",
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8 "requirements":"in-frame codon alignment and a phylogenetic tree"
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9 },
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10 "fits":{
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11 "Nucleotide GTR":{
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12 "Log Likelihood":-4394.17778442101,
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13 "estimated parameters":47,
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14 "AIC-c":8882.482274823486,
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15 "Equilibrium frequencies":[
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19 [0.2366439508665657]
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20 ],
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21 "Rate Distributions":{
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22 "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,
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23 "Substitution rate from nucleotide A to nucleotide G":1,
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24 "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,
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25 "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,
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26 "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,
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27 "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102
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28 },
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29 "display order":0
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30 },
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31 "Global MG94xREV":{
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32 "Log Likelihood":-4272.739394378317,
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33 "estimated parameters":54,
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34 "AIC-c":8653.980859587502,
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35 "Equilibrium frequencies":[
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98 "Rate Distributions":{
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99 "non-synonymous/synonymous rate ratio for *test*":[
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100 [0.2936035676191999, 1]
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101 ]
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102 },
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103 "display order":1
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104 }
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105 },
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106 "timers":{
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107 "Total time":{
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108 "timer":816,
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109 "order":0
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110 },
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111 "Model fitting":{
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112 "timer":12,
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113 "order":1
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114 },
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115 "MEME analysis":{
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116 "timer":803,
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117 "order":2
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118 }
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119 },
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120 "tested":{
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121 "0":{
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122 "TREESPARROW_HENAN_1_2004":"test",
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123 "TREESPARROW_HENAN_3_2004":"test",
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124 "Node6":"test",
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125 "TREESPARROW_HENAN_4_2004":"test",
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126 "Node5":"test",
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127 "CHICKEN_HEBEI_326_2005":"test",
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128 "SWINE_ANHUI_1_2004":"test",
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129 "TREESPARROW_HENAN_2_2004":"test",
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130 "Node12":"test",
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131 "Node10":"test",
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132 "Node4":"test",
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133 "CHICKEN_HONGKONG_915_97":"test",
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134 "GOOSE_HONGKONG_W355_97":"test",
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135 "DUCK_HONGKONG_Y283_97":"test",
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136 "Node19":"test",
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137 "Node17":"test",
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138 "HONGKONG_1_97_98":"test",
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139 "Node16":"test",
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140 "HONGKONG_1_538_97":"test",
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141 "Node15":"test",
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142 "Node3":"test",
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143 "DUCK_GUANGZHOU_20_2005":"test",
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144 "GOOSE_SHANTOU_2216_2005":"test",
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145 "Node26":"test",
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146 "PEREGRINEFALCON_HK_D0028_2004":"test",
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147 "Node25":"test",
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148 "CK_HK_WF157_2003":"test",
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149 "Node24":"test",
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150 "Node2":"test",
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151 "HUMAN_VIETNAM_CL105_2005":"test",
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152 "DUCK_VIETNAM_376_2005":"test",
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153 "Node33":"test",
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154 "HUMAN_VIETNAM_3062_2004":"test",
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155 "Node32":"test",
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156 "MALLARD_VIETNAM_16_2003":"test",
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157 "Node31":"test",
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158 "Node1":"test",
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159 "CHICKEN_CK_160_2005":"test",
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160 "DUCK_VIETNAM_272_2005":"test"
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161 }
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162 },
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163 "input":{
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164 "file name":"/tmp/tmpv_gXOY/job_working_directory/002/2719/working/meme_input.fa",
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165 "number of sequences":21,
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166 "number of sites":566,
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167 "partition count":1,
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168 "trees":{
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169 "0":"(((((((TREESPARROW_HENAN_1_2004:0.0111334,TREESPARROW_HENAN_3_2004:0.00619375)Node6:0.000995666,TREESPARROW_HENAN_4_2004:0.00435165)Node5:0.00226776,(CHICKEN_HEBEI_326_2005:0.0210089,(SWINE_ANHUI_1_2004:0.00770239,TREESPARROW_HENAN_2_2004:0.00906278)Node12:0.00209522)Node10:0.00388724)Node4:0.00340492,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1,DUCK_HONGKONG_Y283_97:0.00279842)Node19:0.00289977)Node17:0.00130638,HONGKONG_1_97_98:0.00384493)Node16:0.000182536,HONGKONG_1_538_97:-1)Node15:0.0209617)Node3:0.00313061,(((DUCK_GUANGZHOU_20_2005:0.00629939,GOOSE_SHANTOU_2216_2005:0.00620784)Node26:0.00253061,PEREGRINEFALCON_HK_D0028_2004:0.0036083)Node25:0.0032889,CK_HK_WF157_2003:0.0066313)Node24:0.0046553)Node2:0.0116809,(((HUMAN_VIETNAM_CL105_2005:0.00652152,DUCK_VIETNAM_376_2005:0.00787762)Node33:0.00196789,HUMAN_VIETNAM_3062_2004:0.0016414)Node32:0.000312551,MALLARD_VIETNAM_16_2003:0.00324422)Node31:0.000412598)Node1:0.000340091,CHICKEN_CK_160_2005:0.00616834,DUCK_VIETNAM_272_2005:0.0094653)"
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170 }
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171 },
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174 "name":"meme.filter.default",
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816 "original name":"CHICKEN_HEBEI_326_2005",
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1447 },
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1448 "GOOSE_HONGKONG_W355_97":{
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1449 "original name":"GOOSE_HONGKONG_W355_97",
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1450 "Nucleotide GTR":0,
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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1869 },
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rdvelazquez
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1870 "DUCK_VIETNAM_376_2005":{
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rdvelazquez
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1871 "original name":"DUCK_VIETNAM_376_2005",
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rdvelazquez
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1872 "Nucleotide GTR":0.008353464800246744,
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rdvelazquez
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1873 "Global MG94xREV":0.008507588898480372,
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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1883 "EBF site 21 (partition 1)":0.9151882402794148,
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rdvelazquez
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1884 "EBF site 26 (partition 1)":0.9573351401140932,
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rdvelazquez
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1885 "EBF site 27 (partition 1)":0.8867197988168598,
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rdvelazquez
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1886 "EBF site 28 (partition 1)":1,
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rdvelazquez
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1887 "EBF site 32 (partition 1)":0.9462700079742482,
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rdvelazquez
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1970 "EBF site 222 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1971 "EBF site 224 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1972 "EBF site 226 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1973 "EBF site 228 (partition 1)":0.9007558657573438,
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rdvelazquez
parents:
diff changeset
1974 "EBF site 230 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1975 "EBF site 231 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1976 "EBF site 233 (partition 1)":0.9579320644469356,
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rdvelazquez
parents:
diff changeset
1977 "EBF site 235 (partition 1)":322.7347759782938,
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rdvelazquez
parents:
diff changeset
1978 "EBF site 236 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1979 "EBF site 237 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1980 "EBF site 240 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1981 "EBF site 241 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1982 "EBF site 242 (partition 1)":3.593458681512879,
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rdvelazquez
parents:
diff changeset
1983 "EBF site 250 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1984 "EBF site 253 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1985 "EBF site 254 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1986 "EBF site 256 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1987 "EBF site 258 (partition 1)":0.9575860982877624,
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rdvelazquez
parents:
diff changeset
1988 "EBF site 265 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1989 "EBF site 268 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1990 "EBF site 271 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1991 "EBF site 278 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1992 "EBF site 279 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1993 "EBF site 282 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1994 "EBF site 283 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1995 "EBF site 288 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1996 "EBF site 291 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1997 "EBF site 293 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1998 "EBF site 296 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
1999 "EBF site 298 (partition 1)":0.3723346163223445,
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rdvelazquez
parents:
diff changeset
2000 "EBF site 302 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2001 "EBF site 304 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2002 "EBF site 306 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2003 "EBF site 309 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2004 "EBF site 311 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2005 "EBF site 312 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2006 "EBF site 315 (partition 1)":0.9573908390602411,
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rdvelazquez
parents:
diff changeset
2007 "EBF site 317 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2008 "EBF site 327 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2009 "EBF site 328 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2010 "EBF site 329 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2011 "EBF site 331 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2012 "EBF site 332 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2013 "EBF site 336 (partition 1)":0.07737790620602035,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2014 "EBF site 338 (partition 1)":0.6815814401903888,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2015 "EBF site 339 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2016 "EBF site 341 (partition 1)":0.8241912078366742,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2017 "EBF site 342 (partition 1)":0.95742755918444,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2018 "EBF site 344 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2019 "EBF site 348 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2020 "EBF site 351 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2021 "EBF site 353 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2022 "EBF site 354 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2023 "EBF site 357 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2024 "EBF site 358 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2025 "EBF site 361 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2026 "EBF site 362 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2027 "EBF site 369 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2028 "EBF site 375 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2029 "EBF site 377 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2030 "EBF site 379 (partition 1)":1,
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rdvelazquez
parents:
diff changeset
2031 "EBF site 433 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2032 "EBF site 384 (partition 1)":0.9121536181285803,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2033 "EBF site 389 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2034 "EBF site 403 (partition 1)":0.9571419936755389,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2035 "EBF site 408 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2036 "EBF site 417 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2037 "EBF site 424 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2038 "EBF site 429 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2039 "EBF site 431 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2040 "EBF site 440 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2041 "EBF site 441 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2042 "EBF site 445 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2043 "EBF site 454 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2044 "EBF site 462 (partition 1)":0.9206163412292598,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2045 "EBF site 466 (partition 1)":0.836317738397839,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2046 "EBF site 471 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2047 "EBF site 473 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2048 "EBF site 477 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2049 "EBF site 478 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2050 "EBF site 485 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2051 "EBF site 479 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
diff changeset
2052 "EBF site 481 (partition 1)":1,
a7305e34418f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
rdvelazquez
parents:
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2053 "EBF site 488 (partition 1)":1,
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rdvelazquez
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2502 },
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2503 "DUCK_GUANGZHOU_20_2005":{
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2504 "original name":"DUCK_GUANGZHOU_20_2005",
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2924 },
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2925 "SWINE_ANHUI_1_2004":{
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2926 "original name":"SWINE_ANHUI_1_2004",
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2927 "Nucleotide GTR":0.01028807762625412,
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3346 },
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3347 "HONGKONG_1_97_98":{
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3348 "original name":"HONGKONG_1_97_98",
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rdvelazquez
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3770 "original name":"TREESPARROW_HENAN_3_2004",
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3771 "Nucleotide GTR":0.006658325208899179,
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rdvelazquez
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rdvelazquez
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rdvelazquez
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3979 },
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3981 "original name":"PEREGRINEFALCON_HK_D0028_2004",
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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7553 "Node33":{
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rdvelazquez
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9230 }
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9231 }
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9232 },
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9233 "MLE":{
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9234 "headers":[
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9235 ["alpha;", "Synonymous substitution rate at a site"],
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diff changeset
9236 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
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9237 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
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9238 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
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diff changeset
9239 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
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diff changeset
9240 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
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diff changeset
9241 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
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diff changeset
9242 ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the &beta;<sup>+</sup> rate"],
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diff changeset
9243 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
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9244 ],
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9245 "content":{
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9246 "0":[
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9247 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9249 [3.518153136581004e-17, 3.243045519502881e-17, 1.022166200682819e-08, 1.291751771813077, 0.999999989778338, 0.5894186108086057, 0.4058674930166563, 1, 0.3590955405423049],
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9251 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9252 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9253 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9254 [0, 0, 1.015244473805534e-08, 2.805293595854978, 0.9999999898475552, 1.564165559839974, 0.2310493931422519, 2, 0.7798467493791119],
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9255 [3.097517451103013, 3.633546560692318e-13, 0.006739028294327419, 0, 0.9932609717056726, 0, 0.6666666666666666, 0, 0.3592491319023247],
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9256 [0, 0, 1.066894692458495e-08, 2.051552228725943, 0.9999999893310531, 0.4229558324457479, 0.4514150344986089, 1, 0.5703133313001572],
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9257 [0, 0, 1.001269178443788e-08, 3.944223233914665, 0.9999999899873082, 2.43042776936683, 0.144470531376273, 1, 1.096459091757323],
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9258 [4.145693582901539, 1.893694670765467, 1, 1.728430979317008, 0, 0, 0.6666666666666666, 0, 1.007246616185795],
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9259 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9260 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9261 [0, 0, 1, 0, 0, 0, 1, 0, 0],
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9262 [6.93484933547672e-17, 6.392567688995331e-17, 1.030030625693157e-08, 0.9290606906239126, 0.9999999896996937, 0.429003806262461, 0.4496226523843093, 1, 0.2582706353881744],
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9263 [4.073331916826687, 1.964429091966281e-13, 0.006739408681290566, 0, 0.9932605913187095, 0, 0.6666666666666666, 0, 0.4724237968534862],
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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rdvelazquez
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9813 ]
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rdvelazquez
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rdvelazquez
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rdvelazquez
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diff changeset
9816 }